Results for the local campaign (PhD Chapter 1)


This series of files compile all analyses done during Chapter 1 for the local campaign (2014):

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

2014 2016 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2016 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

We selected variables and characteristic species (see IndVal index and SIMPER procedure) for these analyses:

Here, we use data from subtidal ecosystems (see metadata files for more information).

Only stations that have been sampled both for abiotic parameters and benthic species were included.


1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity.

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Bneo

Pste

Ssol

Epar

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Organic matter

Grain-size

Heavy metals

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by condition
Phylum HI R
Annelida 20340 1042
Phoronida 1138 2
Arthropoda 871 746
Mollusca 341 725
Platyhelminthes 5 0
Echinodermata 4 139
Hemichordata 2 0
Brachiopoda 0 0
Cnidaria 0 0
Nematoda 0 0
Nemertea 0 5

2.3. Species estimation curves

2.4. Principal Component Analysis

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

2.5. Non-metric Multidimensional Scaling

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species are deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 
##  1  2  1  1  1  1  1  1  1  1  1  1  1  1  1  3  2  2  2  1  2  2  2  2  2  3  2  2  2  3  3  2  3  2  3  2 
## 37 38 39 40 
##  2  2  2  2

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  1  1  3  3  3  3  3  2  3  3  2  2  2  3  2  3  2  3 
## 37 38 39 40 
##  3  3  3  3

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 
##  1  2  1  1  1  1  2  1  1  1  2  3  2  2  2  3  3  2  2  2  2  2  2  3  2  3  3  3  3  3  3  3  3  3  3  2 
## 37 38 39 40 
##  2  3  3  3

Species

Stations with no species are deleted from this analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  1  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2 
## 37 38 39 40 
##  2  2  2  2


Elliot Dreujou

2019-11-22